12-120017960-A-G

Position:

• chr12-120017960-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001367886.1(BICDL1):​c.645+19224A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0442 in 152,236 control chromosomes in the GnomAD database, including 227 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.044 (227 hom., cov: 32)
• Consequence: BICDL1 NM_001367886.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.862

Genes affected

BICDL1 (HGNC:28095): (BICD family like cargo adaptor 1) Predicted to enable dynactin binding activity and small GTPase binding activity. Predicted to be involved in Golgi to secretory granule transport; neuron projection development; and vesicle transport along microtubule. Predicted to be located in centrosome. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BICDL1	NM_001367886.1	c.645+19224A>G		intron_variant		ENST00000548673.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BICDL1	ENST00000548673.6	c.645+19224A>G		intron_variant		2	NM_001367886.1	A1
BICDL1	ENST00000546420.5	c.*101+18048A>G		intron_variant, NMD_transcript_variant		1
BICDL1	ENST00000397558.6	c.645+19224A>G		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.0442 AC: 6726 AN: 152118 Hom.: 227 Cov.: 32

Gnomad AFR AF: 0.0119

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0336

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.0366

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0720

Gnomad OTH AF: 0.0407

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0442 AC: 6727 AN: 152236 Hom.: 227 Cov.: 32 AF XY: 0.0412 AC XY: 3070 AN XY: 74438

Gnomad4 AFR AF: 0.0118

Gnomad4 AMR AF: 0.0335

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.000578

Gnomad4 SAS AF: 0.0304

Gnomad4 FIN AF: 0.0366

Gnomad4 NFE AF: 0.0720

Gnomad4 OTH AF: 0.0403

Alfa AF: 0.0639 Hom.: 726

Bravo AF: 0.0411

Asia WGS AF: 0.0150 AC: 52 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.0
DANN	Benign	0.65

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs11064994; hg19: chr12-120455764;